Cyber Shinji
by animefan29
Summary: A young Shinji makes a wish. A wish that came true thanks to alien technology. Now he is the greatest weapon of alien design who pilots the greatest weapon of human design. But what will he do when he finds his true enemy is closer then he thinks?
1. Chapter 1

**Cyber Shinji**

**Disclaimer:** If I owned Evangelion then Shinji would not have been screwed over.

* * *

After the global event of Second Impact much of the world's geography, climate, and ecosystems changed. The rising sea levels submerged many of the coastal cities including Tokyo, New York, Hong Kong, and Sydney. The most northern and southern regions of the poles became lands with an everlasting if mild winter. Countries that were closer to the equilateral zones experienced everything from chilly spring to blazing summer.

That was as true in Japan that was considered a summer country, the sound of cicadas ever droning in the background, and the trees forever green.

Within one of these ever dressed forests near the home of a long retired teacher strode Shinji Ikari.

Despite all the time he spent out in these woods when he wasn't in lessons Shinji knew very little about the land around him.

He knew that many of the plant, animal, and insect species became extinct after the meteor hit the South Pole, but he could barely name a handful of them.

No it was not nature that the ten year old sought outside but the solitude it brought.

It was funny. Shinji hated being alone, yet whenever his lessons and chores were over he would go out and walk the same path. He may not be a mountain man of any sort but he knew the position of every single rock, tree, and stream that were along this stretch of land.

The reason Shinji walked this path was very simple. While he hated being alone and in fact craved human interaction, it was human interaction that scared him more. The fear that someone would come along, become part of the boy's life only to one day up and leave never to be seen again was the greatest fear Shinji had. So while the path was lonely it was at least familiar and unchanging. A place where Shinji could go and find everything the way he left it. And that brought him comfort. And on any ordinary night he would never dream to deviate from that path.

But then this wasn't an ordinary night, and Shinji would soon find himself departing this little path in the woods but also the path his life had been walking. Thus forever altering the course of human history.

* * *

Like many other nights Shinji was alone in the forest that surrounded the home of his teacher. Never his home, just the place he lived.

He was sitting on a large rock outcropping that he used to mark the end of his secret trail. Not once had he ever taken a step past these rocks.

They were as lonely as any other part of the woods but they were also the most unchanging, so they were the most comforting.

It was here Shinji went when he left his teacher's house, never anywhere else. And it was here that Shinji thought about his life.

Six years.

It had been six years since his mother died and he last saw his father. Not once had his old man tried contacting him. Not one visit. Not one letter. Not even a single phone call.

Shinji tried asking his teacher about his father but the man knew little about Gendo Ikari or was ordered not to say anything.

To this day Shinji could not understand why his father left him. Maybe it was because he was so average.

Shinji was, according to him, the very definition of mediocrity, and in many ways he was. Although his teacher would argue that the boy had talent playing the cello.

But he was not fast, nor was he strong and his ability to play sports was virtually non-existent. Intellectually he a good student.

Some people would call him bright when he applies himself but they would never think of using genius to describe him. The most advanced mathematical problems he could work were long division. He could barely play a computer game much less write a computer program. And his lingual skills were limited to Japanese.

Perhaps that was why Gendo had left him. After all his one of the few things his teacher knew about his parents was that both of them were geniuses. It was common knowledge in the world of academia that Yui had written some of the best papers on how to make theoretical robotics practical by using biomechanical engineering, and even though she pursued the life of a scientist she was stilled hailed as an artistic prodigy when it came to the piano. Gendo was not quite as well known but his work in the field of biology since his work never went public, but anyone who knew him in college could tell you that if he had been part of the cloning projects of the late nineteenth century the clones would have been perfect. He was also hailed as one of the greatest chess players to ever attend Tokyo University.

Shinji was just an ordinary boy.

Looking up to the stars Shinji saw a shooting star. Despite knowing that a shooting star was just a meteor burning up in the upper atmosphere he still decided to go along with the old tradition of making a wish. Closing his eyes he concentrated on what he desired. The wish he made was not for his mother to be brought back to life or even for his father to come back into his life. He knew the former was impossible, and something told him that wishing for the latter would be pointless. No, his wish was in essence simpler. Shinji wished that something would happen that would help him change, to become different.

Shinji kept his eyes closed concentrating on that desire, and then he heard it. It was a slight rumbling, similar to the kind of sound airplanes produced when they came in for a landing. Yet this wasn't quite the same.

Shinji opened his eyes and they immediately bugged out. The shooting star was still visible, meaning it wasn't burning up the way it was supposed to. It was also heading straight towards him.

Thoughts and images of another impact suddenly ran through the young boy's mind as he watched the fiery rock of death fly towards him and he did the only thing he could do. He ducked and covered behind the rock he was sitting on, which put him right in-between several other rocks.

It was a pretty good spot to hide as the stones were just a small part of much larger rocks that were in the ground, making them very stable. That was very fortunate as when the meteor crashed several seconds later it caused a strong tremor that knocked over a few trees but didn't even shake the stones loose. Add that to their density they made very good shields from any flying debris, of which there were quite a bit formed from loose rock, dirt, broken off branches, bark, nuts, and the like.

When things had quieted down Shinji stuck his head out of his makeshift shelter. The meteor had struck earth about thirty meters away, and from the looks of it went another hundred meters, if the path of destruction was any sort of indication.

Shinji's first instinct told him to run back to his teacher and to the safety of the house. But another part of his mind couldn't help but notice how big of a coincidence it was that he wished for something to happen to make him different and a space rock nearly lands on his head.

On the one hand was the sense of reality and pessimism that the early loss of his parents from death and abandonment brought him. On the other was the child like sense of adventure that had been sown when his mother was alive. The desire, no, the need to seek out the unknown and examine it until you knew it inside and out. A drive for knowledge that Yui believed that humans needed to live, to advance, to grow, to learn, to evolve. A final parting gift she left in her son, and that eventually won out against the more practical and fearful side Shinji's psyche.

So, repeating the mantra '_I mustn't run away, I mustn't run away, I mustn't run away,_' over and over in his mind he climbed out from between the rocks and walked towards the crash site. A new path that took him away from the old an familiar.

The destruction caused by the meteor was a very easy trail as it started out as several meters wide turned over dirt with a number of fallen trees along the edge. The farther the trail went the narrower it got.

When he finally reached the end Shinji was a little confused by what he saw. Dug into the dirt was a small round black sphere about the size of a baseball. Now Shinji was not an expert on geology but he did know enough that rocks were only supposed to be smooth when they were submerged in running water, or were smoothed by man. And that the there was no way you could find such a perfect sphere in nature, that was not shaped by man first.

Shinji jumped down into the newly made ravine to take a closer look. Upon closer inspection Shinji's first thought was that it might be a satellite that had fallen from space, but those weren't made for reentry. He might have thought it was a new design but after Second Impact the nations of the world had lost all interest in space in favor of dealing with the plethora of new problems here on Earth.

Noticing a slight oddity, Shinji stuck his hand out and hovered it close to the sphere's surface. From what he could tell there was no ambient heat. The inquisitive side in him seeking knowledge forced Shinji to do just about one of the dumbest things anyone could do with an object that just fell from space according to conventional knowledge. He touched it with his finger.

The sphere was warm, but nowhere near as hot as it should be. Shinji estimated as only about 38 degrees Celsius, just a little over the human body temperature.

Taking his finger away he noticed a small black smudge where he touched the sphere. Shifting his gaze he saw that the sphere was not black, just covered in a substance similar to soot.

Once again letting his curiosity control him Shinji reached down and grasped the sphere in both hands. Lifting it up, he started rubbing it clean with his formerly white shirt. With the unknown object clean he gave it another inspection.

The color could only be described as metallic silver, its shine being almost hypnotic as Shinji contemplated what mysteries lay within it. Unintentionally Shinji, in the heat of the moment of this incredible find, let a single word slip between his lips that described this situation and the artifact he held. "Wonderful." That is when everything changed

That word combined with Shinji's touch were the keys needed to unlock the sphere's secrets. One of which was that it wasn't a sphere.

Shinji eyes widened and he gasped in horror the artifact's shape suddenly warped and shifted, before it stretched and thinned as it started crawling up his arms. He tried throwing it away but it had already latched onto the boy.

He screamed in terror as the liquid metal slithered over his skin towards his head. He grasped at it desperately as he tried pulling it off but like water it slipped through his fingers. Nothing he did could stop the metal from completing its objective.

Upon reaching Shinji's head the metal began flowing into the boy through any means. Shinji tried stopping in by shutting his mouth as he continually tried to pull it away, but it was to no avail. There was no space small enough that could impede the substance.

It slithered through the shut lips and clenched jaw. Up the nose and in the ears. Across and around the eyes. On the inside the liquid metal split apart to different parts of Shinji's body. Some began traversing the intestinal track. Some spread over the muscles and skeletal structure. Some more traveled to the skin and major organs. The last bit went straight for the brain as it was the most important part.

The liquid metal, in actuality nanites just a little smaller then the cells in the human body, began the process they were programmed to do. Unfortunately due to a lack of proper resources and the emergency assimilation they could not complete process in a single cycle. Instead the host would have to be made unconscious while they began the preliminary procedures then use any materials the body ingested over a number of cycles continue the process. It would take awhile but soon enhancement would be complete.

Shinji's worry increased as he felt an unusual sensation in his head. The sensation was like the pressure one felt when they were wrapped tightly in a thick comforter. His thoughts became hazy and his eyelids heavy. Despite his mental protests Shinji felt his body lower itself to the ground as his eyes closed. His breathing became deep and relaxing. Shinji's body was putting itself to sleep and Shinji was afraid that it would never wake up.

* * *

Sometime later Shinji groggily reopened his eyes. '_Was everything a dream?_' Were his first thoughts.

Thoughts that were dashed to pieces the moment he saw the crash site around him that he had fallen asleep in.

Patting frantically at his body Shinji couldn't find a trace of the liquid metal.

As soon as he thought of the '_liquid metal_' information flooded Shinji's mind. Without any logical reason he could think of he suddenly knew that the substance was a colony of trillions of microscopic machines called nanites that were designed to integrate with a host body and then enhance it.

Seeking a greater explanation new information was downloaded into his brain. The nanites were created originally as a military weapon used by a surprisingly human like race of aliens against an unusual enemy that they encountered in their exploration of space. As the war continued the technology used to produce the nanites was continually enhanced and the military was given the latest models while older ones went to civilians in the hope that it would help them survive in case of emergency.

The information told Shinji that the nanites in his body were part of an experimental project that would hopefully turn the war in their user's favor. However before the experiment could be moved into its final phase of testing the war cruiser the laboratory was kept on came under attack by an enemy assault unit. Overwhelmed the cruiser was close to destruction when the scientist in charge of the project launched the prototype out into space as well as a transmission to the nearest military base containing the nanites secrets.

In the vacuum of space the nanites remained dormant until they began atmospheric reentry where they needed to activate to survive. After landing an emergency program was initiated that would cause the nanites to assimilate with any organism that matched the genetic profiles they were programmed with used vocal communication, something the enemy has never shown the capability to do.

Shinji then used that information and made two hypothesis of why the nanites would integrate with him. Either they were damaged at some point thus resulting in the program experiencing digital detritions, or Shinji's DNA was similar enough to the nanites creators that they couldn't tell the difference.

Shinji stopped and blinked. Those were not normal thoughts for a ten year old boy who could barely use the more complicated word processing programs.

Looking at his watch to figure out how long the nanites had him knocked out he almost had a heart attack. He had been asleep for an hour! It was just a few minutes until curfew.

Getting up from the ground he raced through the woods back to his path. Then running down that path which was clear of obstacles he made it back to the edge of civilization that was his teacher's house just scant seconds before his curfew was up. Standing at the door was his teacher who gave Shinji a light reprimand for nearly missing curfew. There would be no punishment but he didn't want Shinji to do it again.

Shinji got ready for bed quickly not wanting to risk his teacher's ire. As he settled down Shinji wondered what was going on with the nanites that were now a part of him. As if in answer Shinji knew now the primary mental connection was established every time he went to sleep the nanites would induce a near coma like state so that he would not feel the alterations that they were doing to his body. The coma would only last the normal amount of time the body needed for rest, which the nanites will know as they will be constantly monitoring him. The number of times these cycles of enhancement would continue was not determinable, but until then Shinji would feel an increase in hunger as his body would be needing a larger amount of nutrients both to serve as energy for the body and to serve as the material the nanobots used to enhance it.

* * *

A month had gone by and the enhancement cycles were complete. In that time several government agencies had come to the area searching for the extraterrestrial object that they had detected. The people sent to retrieve it had found the crash site but were unable to locate the cause.

They questioned Shinji and his teacher as they were the closest living people to the crash, but they were unable to find out any solid leads to what happened to the meteor. It didn't help that they had very little equipment and manpower compared to what they had before the year 2000, but that's what happens when priorities change.

Speaking of changes, the nanites enhancements had a dramatic effect on the boy. The nanites had two primary objectives to complete before the enhancements were finished. The first was the conversion of portions of Shinji's brain so that it could be used as control center for the nanites once everything was finished. The second objective was to change Shinji's body so that was composed of an organic metal.

Even though it sounded contradictory, it was an incredible advancement in nanite technology. It combined several different nanite enhancements combined with a new integration process to create a material that was both organic material that imitated metal and metal that imitated organic material.

With the nanites Shinji could then change the properties of his body to complete specific tasks, within certain limitations.

The most basic of his abilities included his enhanced strength and speed. Combine that with his new computer like ability to retain information, compute mathematical formulas, and his machine like precision and he had become a genius both on the sports field and in the classroom. Although he did improve both those aspects in his life he did keep most of his new mental and physical abilities a secret. Didn't need people asking too many questions now did he?

And with the nanites' ability to change any aspect of his body, including themselves, they had numerous uses that Shinji only needed to do a bit of experimenting before he discovered them. Although there was only so much programmed into the little buggers. If Shinji wanted them to do anything that wasn't he would first figure out what changes needed to be undergone himself before he could order the nanites to make it happen. So he did a lot of studying on anything that pertains to machines, fortunately the nanites provided him with detailed schematics on their inner workings.

But what was probably the most important aspect of the nanites was their ability to replicate themselves. This was a feature that previous nanite models were incapable of, so if anyone needed or wanted nanites they had to go to the proper facilities, making said facilities targets in the war.

Shinji's nanites however were capable of constructing the microscopic components they were comprised of, then assembling them. Then once the nanites were uploaded with the proper programming they could be configured to serve a purpose in Shinji or be left in storage until they were needed. If he wanted to Shinji could even inject the nanites into someone else making them like him, as that was the original purpose of this specific feature. To help spread what was probably one of the best weapons to defeat the Enemy.

But Shinji is hesitant about granting people the nanites. They were a very powerful force, and in the wrong hands could spell disaster. Hopefully someday in his life he will meet someone he trusts enough to give this gift to.

* * *

(Time Skip – 4 years)

"We're sorry but due to a state of emergency in the Kanto and central Tokai region all phone lines are down. Please hang up and head to your nearest shelter. This is a recording."

Shinji was very tempted to fry the phone systems. Of course this was a state of emergency. Why else would the train station and the entire city around it were deserted? Why else would someone dial the emergency phone line? To wish the operator a happy birthday!?

Sighing Shinji reigned in on his more destructive impulses and instead focused on something more constructive.

Listening in on the military radio channels might prove useful if the low flying fighter jets were any sort of indication but for some reason the JSSDF had changed their codes early and he was still trying to crack it. All he knew was that something big was going on.

He tried accessing the internet wirelessly but it seemed that the government had shut that down as well. So no chance finding any leaked info there. Sure most of the rumors you hear on the internet were more or less a waste of time, but if you knew how to sift through the info you could find something worthwhile.

Sighing at the fact that two of his most useful information gathering techniques he did about the only thing he could do. He looked at the letter he had been sent and the picture that came with it.

After ten years without sending anything to indicate the man even knew that he existed, Shinji had suddenly received a letter from his father. The letter was simple in its content. It was merely a set of instructions to take the train to this station where he would be picked up by one Capt. Misato Katsuragi. On the back of the letter was one hand written word, "Come."

Shinji would have ignored it but apparently his teacher had known and already prepared Shinji's things. Next thing Shinji knew he was on the train to meet this Misato.

Looking at the photo of said woman Shinji had to wonder what exactly the woman did. Considering her figure, and how she unashamedly flaunted it in her photo he was a little worried. So before he left he managed to download all the public records there were to be had on the woman. But the confusing thing was except for her college records just about everything on the woman was classified.

Shinji found this interesting and decided to check to see what he could find on his father to be working with such a person. Unsurprisingly he could find just about anything he wanted on the man up until just after his marriage to Yui. The oldest thing he could find was that in the year 2000 he had joined the Katsuragi expedition to Antarctica. Although the mission itself was classified it did say that he was only one of two survivors because he left the site the day before Second Impact.

The other survivor being Misato Katsuragi who had survived by being put into a life raft that was designed to survive explosions.

Speaking of the woman, she was several hours late

Getting that feeling he was being watched Shinji looked down the street. There at the end was a girl his age. A girl whose appearance caused Shinji to forget just about everything. Her skin was pale and she had red eyes like an albino but something was wrong. An albino's entire eye was red, not just the iris. And they had white hair, never the shade of light blue that gave her an exotic air.

A flock of birds taking off distracted Shinji for less than a second, but when he turned back the girl was gone. Getting back to his senses Shinji started berating himself for zoning out like that. That girl was an anomaly and he would normally examine such things. Such as how she appeared without him noticing, and what she was doing here. Considering how she just disappeared he would guess that it was some sort of illusion and he would have known if he had done scans. But now all he had was his visual memory of her which was useless for the scans he needed to do.

Calling up said memory file from his computer like brain he zoomed in on her face. Taking care to maintain his focus Shinji noticed something that made him gasp. The girl was almost an exact copy of his mother!

Calling up a memory file he had of his mother that he managed to find he set to comparing them. If you factored out their age difference, hair color and style, eye color, and skin tone and you would have an exact match. But not even people of blood relation looked that close except for twins of the same gender.

Putting the files away Shinji noticed how the number of low flying jets had increased. Feeling a series of tremors in the ground he looked to the nearby mountain. Just as a giant green monster with a bird skull for a face walked by, being harassed by a number of VTOLs.

This time Shinji didn't let his shock stop him from scanning. Using the various optic scanners he had enhanced his eyes with Shinji first scanned with thermals, then for any ambient radiation, zoomed in to find any unusual physical features that would be too small to see from this distance, and basically scanning with every other tool that uses visual.

Shinji gasped at what his preliminary scans showed. This was the Enemy!

The very same Enemy that the nanites were designed to fight, only on a much bigger scale then what he had in his database. The Enemy the nanites were effective against were generally human sized even if they varied in shape. But this thing looked like it could take on a battle cruiser and win on its own.

So what the heck was it doing here on Earth? In a quadrant of space that was several hundred light years away from the war.

Shinji watched in a mixture of awe and terror as the VTOLs launched a barrage of missiles that smashed into the giant and exploded, but as the smoke cleared their wasn't a single scratch on it.

Then the giant lifted its arm and a lance of light flew from it, striking and destroying one of the VTOLs. The remains of the craft crashed only a few meters away from Shinji but still he did not move.

While the beast was distracted another salvo of much larger missiles launched from several gunships flew towards it. This struck a wall of orange light shaped into hexagons.

Pointless Shinji thought. This particular Enemy had a thick hide so most weapons would just bounce harmlessly off it. And even if they did throw something strong enough that could actually hurt it, they would be countered by the energy barrier that the Enemy could naturally generate. All currant Earth weapons were useless as anything more than a distraction.

Hearing the screeching of car tires, Shinji turned to see a blue Renault raced down the abandoned street. Stopping right next to him the driver's door opened revealing the form of Capt. Katsuragi.

"Get In!" She shouted. "Sorry I'm late."

Shinji didn't bother to respond as he calmly walked around and got in on the passenger side.

Misato stepped on the gas and the car peeled away just as the giant stepped onto the spot it had just rested.

As the car made its way away from the behemoth Shinji decided that there was just a little too much coincidence for his liking. The letter telling him to come on this day. The sudden appearance of the Enemy. Deciding to that the best way to get info right now was conversation he spoke up.

"So Capt. Katsuragi…"

"Oh please call me Misato."

"Alright Misato."

"Say, you're awfully calm given the situation." The driver commented, sounding pretty calm herself.

"I wouldn't say I am calm but I must ask. What is that thing?" He already knew but he needed something to base the woman off of.

"That thing is an Angel." Misato said, not keeping a slight sound of disgust and hatred out of her voice.

Shinji looked at her skeptically. Angels were what his people were calling it? The creators of the nanites had many names for them, the Enemy being the most common, but they were never called by the names of beings that were supposed to be protectors and saviors of the soul. But he better get used to it since he had a feeling that he was being involved with them.

But why? Why would they come to an unassuming teenager when they were dealing with a threat of this magnitude? Did they find out about the nanites? No that was impossible. He had done everything he could to keep a secret. So why?

They had made it a considerable way away from the city the car slowed to a stop.

"Why are we stopping?" Shinji asked nervously. She wanted to stop in the middle of a war zone? And the fact that she drove like a maniac. He ran the numbers and the statistics of him surviving if he didn't have the nanites were shockingly low. Not very comforting.

"Oh just taking a look." Misato responded as she took out some binoculars, and started scanning the area they just left.

Shinji followed suite and zoomed in on the area with his optics. What he saw was a large number of aircraft leaving the Angels vicinity. That could only mean one thing.

"Oh no, they're going to use an N2 mine! Get Down!" Misato shouted as she tried to wrap her arms around Shinji and cover him, only to have the boy beat her to the punch line.

The wave of light and air blasted against the car forcing it to take several nasty rolls before stopping on its side.

"Uhh…You alright Misato?" Shinji asked the purple haired woman in his lap.

"Uh, yeah. I'm ok," she replied, "but if I had known you moved this fast I would have worn my special panties." If Shinji's mild blush was any indication she had regained control of the situation.

Crawling out from the side that wasn't facing the ground Misato and Shinji set about to righting the vehicle. To Misato it seemed surprisingly easy for one woman and a thin teenager to push 

over a car, even one as small as hers. But with a good shove the vehicle was back on four wheels.

"Whew, thanks Shinji. You're pretty useful." Complimented Misato.

"Thank you Misato." Responded Shinji as he stared off in the direction of blast.

"Something wrong?" The captain asked seeing Shinji wasn't exactly paying attention to her.

"The N2 mine failed to destroy the Angel." Stated Shinji. The energy released from the blast interfered with his optics but he with a slight adjustment he could see through it. And what he saw was that close to forty percent of the Angel's body had been burned away. Enough to stop it but not nearly enough to kill it. Especially since there was virtually no damage visible on its exposed core.

According to the nanites files there were only two ways to destroy the Enemy. One was to destroy about ninety percent of their body, at which point their ability to operate ceased. Or the second and often easier way was to administer significant damage to the core. Anything else would force the damaged Enemy unit into a state of hibernation with their most powerful energy barrier erected as they focused their power into defense and regeneration.

"Oh no! Just look at my car! I still had 37 more payments on it!" Whined Misato bringing Shinji back to Earth. Again he had to wonder about the woman's mental condition. There was a giant green monster running amok and she was worried about the number of payments were left on her car?

Getting into the car Misato tested to see if it still worked. It didn't.

"Sounds like a problem with the battery." Suggested Shinji, which he confirmed as he looked under the hood. "We can probably get a new battery from that store." He said pointing to a conveniently placed auto parts store.

Misato grinned. "Shinji you're a genius."

A few minutes later the two were back on the road.

"Uh, Misato. When I said 'get a new battery' I meant one." Said Shinji as he gazed over the back seat full of batteries that Misato had relieved from the store.

"Heh heh, well this is an emergency. We never know when we might need another." She explained with a nervous chuckle.

Shinji gave her a look that said he didn't buy it, but he kept his mouth shut. He might be able to use those batteries to power an experiment later.

A short while later the two were in an underground transport system that was carrying the them and the car they were in down below ground level.

"NERV?" Asked Shinji as he looked at the booklet Misato had just handed him.

"Yup," she replied. "It's a secret organization designed to fight the Angels."

"And my father is a part of it?"

"Of course. Don't you know what your father does?"

"My teacher said it was important to mankind, but that was all I was ever told."

"I'm guessing you don't get along with your father?"

"Can't say. I haven't spoken to the man in 10 years." Shinji said as if he was talking about the weather as he looked through the book.

Noticing an increase in light levels he looked up at where they had just arrived. "A Geofront, impressive." He said in an impressed voice.

Misato was a little disappointed. Normally people were awe-struck by the impressive artificial environment.

* * *

"Arrrggg. This is why I hate wearing skirts in this place." Said Misato as they the door way in front of them opened and the pressure change caused the wind to lift up the skirt of her dress.

Shinji ignored it as he pretended to continue reading the booklet. He had already memorized it and was now building an internal map of the NERV facility. A map that told him they were going in circles.

"You know Misato, we've already passed this spot three times." He eventually said.

"Don't worry, they built this place like a maze. That's why they have these walk ways." She responded as she looked at her map.

"It might help if you weren't holding the map upside down." Shinji Suggested.

"What are you talking…Uh, Oops. We need to go this way." She said making a right turn. Shinji right on her heels.

Finally reaching the elevators the door opened to reveal a blond woman wearing a lab coat and a one piece bathing suit.

"Heh heh, Hey Rits." Said Misato nervously.

"Honestly Misato, you still can't find your way around this place?" Ritsuko Akagi said unbelievably. Turning to her companion she said, "So this is the Third Child?"

"Yup." Confirmed Misato.

Shinji this bit of info away for later. Whatever was happening they had been prepared for it for awhile. But it was best to continue playing the role of the polite boy who doesn't know anything. Mainly because that's what he was until he found a computer to hack into. "Hello, I'm Shinji Ikari." He said with a bow.

"Polite isn't he." Commented the doctor.

"Yeah, he's nothing like his father." Said Misato

* * *

After a trip down some mind boggling long escalators, where the doctor made some odd joke involving something called the 09 system being an Oni. Then a river raft trip across a vast room full of an orange liquid which confused Shinji. He had dipped his hand in the substance when the two women weren't looking and according to his scanners the liquid had a composition similar to blood.

They then walked through a pair of armored doors into an unlit room. Maybe they were going for some theatrical drama, too bad Shinji's eyes shifted over to night vision allowing him to see the giant head that resided in the room, the rest of it submerged under the orange liquid.

When the lights came one Shinji was already facing it and showed not a hint of surprise. He remembered Unit one thanks to the nanites enhancing his memories.

"A robot. How surprising." He said in an unsurprised voice.

"It's not a robot. It's the artificial life form Evangelion. Man kind's ultimate weapon and our last hope." Corrected Dr. Akagi.

"And is it what my father has been working on?" Asked Shinji.

"Correct." The answer did not come from the captain or the doctor.

Shinji looked up. There was the man who left him at a train station to be picked up by a stranger ten years ago. In that time they had only seen each other once. Three years ago at the empty grave of Yui Ikari. Not a word had been spoken between the two. They had just stood in respect of their fallen family member. Shinji had been the first to leave.

And now here he was again. Standing behind thick, probably bullet proof, glass on a platform above and behind the purple behemoth.

"It's been awhile Shinji." Said Gendo.

"Father." Curtly greeted Shinji.

Turning to the operations director Gendo and calmly said. "We're moving out."

"Moving out? But we don't have a pilot!" Argued Misato

"A spare has just been delivered."

"What?" Misato's eyes widened as she realized the implications. "Him?" She asked as turned to Shinji. "That's impossible. It took Rei 7 months to synch with her Eva. There's no way he could do it on his first try."

"There's no one else." Said Ritsuko. "He just has to sit in it. We don't expect anything else from him."

Speaking up Shinji said. "It sounds like a suicide mission. After all I've had no training, so what could I do? And what would you do if I refused."

Gendo's response was to contact the deputy commander. "Fuyutsuki wake Rei." He commanded.

"Can she pilot?" Asked the elderly man over the comm. systems.

"We have no choice." Was the response.

Hearing the armored doors open again Shinji looked to see a medical team wheeling in someone on a gurney. His eyes widened as he recognized the girl he saw earlier, but with some drastic changes. She was not wearing the simple green school uniform in his vision but a white, armless, skin tight suit. The suit left nothing to the imagination, especially the injuries that covered her body. The broken arm, the bandages running up both arms, the one that covered her eye.

"Rei, our spare is useless. You must pilot." Commanded Gendo.

"Yes sir." Rei weakly responded.

"You've got to be kidding!" Shouted Shinji. Quickly running the numbers of Rei's survival he paled. "I might die if I pilot, but she will die!"

Gendo turned to his son and said in a cold voice. "You have refused to pilot so you are useless and we have no time to deal with useless people."

Shinji might have responded had the ground didn't suddenly shake from an explosion on the surface. The explosion forced everyone but Shinji from their feet and had knocked several steel beams in the ceiling. Heading straight for Rei who had fallen from her gurney.

Everything that happened next was just a blur to everyone. Shinji acting on instinct rushed to over to the blue haired girl wrapping his arms around her and covering her body with his as he created an armor on his back that was several times harder then steel.

Moments before impact the eyes of the Evangelion glowed and its left hand moved, breaking the restraints, and placed itself between the children and their death.

"The Eva it moved!" Shouted Misato.

"That's impossible, the entry plug hasn't even been inserted!" Ritsuko shouted back unbelievingly despite the evidence before her face.

Misato looked over to the children and wondered aloud. "Did it move to protect him?"

Shinji knew what Unit 01 did but didn't care. He was more focused the girl in her arms. Her breathing was fast and labored. Some of her injuries had started bleeding. She was in a lot of pain. Acting quickly Shinji sharpened and extended his index nail into a needle and punctured Rei's neck, injecting her with medical nanites. They would numb the pain, make the girl unconscious, and then begin repairing any injuries starting with the critical ones. Then once their job was complete they would deactivate and be absorbed by her body. That was all he could do for her right now.

Well almost all he could do.

Looking up to his father he said. "All right. I'll pilot the Eva, but understand Father I am not piloting for you." Under his breath he then whispered something that only Rei would hear that he was sure she would forget when the nanites knocked her out. "I have my own reasons to fight the Angels. One of each now is to keep you safe."

* * *

**Author's Notes:** Well another story added to my archive. I got this idea in my head after reading Shritistrang's Super Smash Bro. The Evangelion Wars. Great story by the way. The main inspiration were the chapters involving the Apareis and that is all you are going to get out of me. You want to know more read the story.

Anyway I was recently encouraged by a correspondent of mine, who is also the inspiration for another of my Eva stories and has been helping me with another, guy should really try writing his own stories what with all the good ideas he has.

To be honest I don't really know where I am going to this will probably be put on the backburner for a while as I work on my other stories or studying. And for those that haven't guessed this will be a Shinji/Rei romantic pairing, but it won't be a romance without trouble.

Anyway I always appreciate feedback on my stories and on more than one occasion has a reviewer become an adviser. So…

**Please Read and Review.**


	2. So Many Secrets

**Cyber Shinji**

**Disclaimer:** If I owned Evangelion then Shinji would not have been screwed over.

"Talking"

'_Thoughts_'

"_Radio_"

* * *

**Chapter Two**

After Shinji decided that he would pilot Dr. Akagi had taken him to get a quick rundown on the Eva operating system. But not before he made sure that Rei was taken by the medics to a safe and secure area.

And now he sat in Unit 01's Entry Plug, A10 clips in his hair, listening to the command crew as they prepped the Evangelion for launch.

"Inserting Entry Plug."

"Plug-in procedure completed."

"Initiating first level interface."

"Flooding Entry Plug."

When those words were said an amber liquid began filling up the Entry Plug. Shinji wasn't particularly worried about it as he had modified his lungs years ago to be able to filter liquids so he couldn't drown. That was back when he couldn't swim. As long as the substance wasn't acidic he would do fine. However his sensors informed him that this was the same substance with the blood-like composition that the Eva had resided in. But still he thought it was important to ask the good doctor what was going on since he hadn't been previously informed of this and as far as NERV knew he couldn't breathe underwater.

"Dr. Akagi, would you mind explaining what you are doing." He requested.

"Don't worry; this is LCL. When it saturates your lungs it will directly oxygenate your blood so you won't drown. It will also provide some cushioning and will help enhance your sync ratio." Explained the faux-blond doctor.

As the LCL rose past his head Shinji calmly inhaled the liquid, filling his mouth and lungs with it. "It tastes like blood." He idly commented.

"Tough it out. You're a boy aren't you?" Said Misato over the speakers. Shinji chose to ignore the woman in favor of beginning his own set of sequences.

His internal systems began an in-depth analysis of the LCL but all the information would be stored away for him to look over later. Right now he had more important things to do.

'_Begin Assimilation Procedures.' _Doing the same as he did with Rei, Shinji injected billions, bordering on a trillion of nanites from his body directly into the Entry Plug. From there a portion that was injected would remain in the Entry Plug while the rest would move on into Unit-01 itself. Considering the size and mass of the Eva Shinji was sending every spare nanite he had into it, and then some. He even sent a few dozen into the A10 nerve clips.

Meanwhile in Central Dogma. "Ma'am, we are getting some irregular readings from the Eva's nervous system." Lt. Shigeru Aoba informed Dr. Akagi.

"What? Let me see." The doctor said leaning over his council. But no sooner did she think of having the Magi run a quick diagnostic did the irregularities cease.

"Is it something that we should worry about Ritsuko?" Asked Misato.

"Probably not. Unit-01 is the test type so there are bound to be a few quirks in the system. But keep me informed if you see anything else."

Back with Shinji. '_Nanite injection sequence complete. Proceed with Level 3 assimilation._' Shinji's assimilation had been a high priority emergency Level 1 due to the circumstances. At Level 1 the nanites were to assimilate with their host as quickly and safely as possible. At the lower priority Level 3 the nanites would first travel through the host mapping anything and everything, making special note of any important organ/computer systems. As this happened the nanites would be relaying all of the gathered data back to Shinji who would be overseeing the process to make sure it happens as it should be. At the same time the nanites will begin using whatever spare materials they find to start reproducing. But until Shinji gives the OK they would not start any modifications.

At the moment it was too risky to start upgrading Unit 01. The last thing he needed right now was for the nanites to shut down some critical system for upgrade in the middle of the upcoming battle. But with the information Shinji was getting he would have a better understanding of how the Eva works.

And one particular bit of information almost made Shinji go bug eyed. The Evangelion Was Alive!

It wasn't a fully biological organism as there were various computer systems, sensors, and equipment built into the body such as the internal battery. But still the majority of it was biological in nature. It just wasn't like any biological organism that Shinji had in his data banks.

No, that wasn't entirely true. Some of the latest data told Shinji that Unit 01's DNA was surprisingly similar to one specific organism. The Angels. '_Oh Hell!_'

It took all of Shinji's self control not to physically react at the information. As shocking as it was he would have to contemplate on how NERV created an Angel, even an incomplete one judging from the inactive genetic sequences, later. Right now he needed to deactivate all the injected nanites to prevent them from initiating one of their core programs.

In the event that the Enemy ever managed to inject one of their numbers with nanites to enhance themselves, not they ever showed particular interest in doing that, the nanites were programmed to attack the body from within. They would be literally breaking the Enemy down cell by cell. Again, in case the Enemy ever actually gained an interest in technology as a safety precaution the program was imprinted as a core program, where it was impossible to remove.

If Shinji wanted to use the nanites in conjunction with Unit 01 in any way shape or form he would have to rewrite the program. Something that would take weeks, if not months to accomplish. Assimilating the Evangelion with the nanites before that time would just be detrimental.

But there was one thing he could do first. Dr. Akagi had told him that he would pilot the Eva by synching with it thus controlling it with his mind instead of using conventional methods. Although they had still installed the butterfly handles to give something for the pilot to hold onto and use as a focus to help them move the Eva. It also provided a nice easy to reach place where they could put some buttons that were needed to operate systems that couldn't be controlled by synching.

The information the nanites had provided gave Shinji gave a basic idea of how the A10 nerve clips worked to enhance his synch ratio, and by using that concept with the nanites he could set up a more powerful system in the hairclip-like devices. It wouldn't be the most elegant or efficient system, but it should raise his synch ratio by at least a few points.

Back on the command bridge.

"The pilot has passed the absolute borderline. Bidirectional circuits are open." Said Lt. Maya Ibuki. "My God!" She exclaimed when she saw the numbers.

"What is it?" Asked Dr. Akagi looking over her assistants shoulders. "That can't be right."

"Rits?"

"According to this, Shinji's synch ratio is currently at 48.3 and rising." Ritsuko told her military counterpart. Typing in a few quick commands the results were verified. "Synchronization ratio is holding at 55.2 with a margin of error of 0.3 percent. Harmonics are normal. We can do this."

"Alright. Begin launch sequence!" Said Misato sending the Eva cage into a frenzy of activity to release the Eva from its restraints and to move it into position on the catapult. "Evangelion Unit-01 Launch!" Misato commanded.

Shinji could feel the G-forces shove him backwards into his seat as the catapult launched Unit-01 upward to the surface. And with only a slight jerk movement ceased, and Shinji was staring down the Angel through the eyes of the Eva.

"_Are you ready Shinji?_" Asked Misato.

"Ready and waiting."

"_All right. Release final safety locks!_" With that order the massive bolts in the Eva's shoulder pylons that kept it attached to the catapult sled were unlocked, freeing mankind's ultimate weapon.

"_OK Shinji for now just focus on walking._" Instructed Ritsuko.

The command crew waited with held breaths as they monitored Unit 01 and its pilot. They each leaned forward unconsciously as the Eva lifted its foot, moved it forward a little, and then heavily planted it back on the ground. The bridge erupted in cheers with Ritsuko crying "He's Walking! He's Walking!"

In the Entry Plug Shinji ignored the hollering NERV personal in favor of keeping his concentration. '_Easy there Shinji. It's not that difficult. It the same as controlling a digital avatar._" In truth there were was a world of difference between controlling a body composed entirely of data in a world of data, and controlling a giant cybernetic alien that is the Eva in the real world. But the basic concept of using your mind to manipulate a body that is not your own was the same.

With that in mind Shinji took two more steps with confidence. Although he was slightly annoyed with the Eva's reaction time. By his estimation the time between his command and Unit 01 moving in accordance took approximately .843 seconds. Unfortunately he didn't have time to work on that as the Angel was suddenly upon him, swinging its arm to knock the Eva aside.

Shinji blocked the attack, which sent jarring reverberation throughout Unit 01. Gritting his teeth he countered with a left hook, only for the Eva's fist to be caught in the Angel's clawed hand. The end of the arm started to glow and an energy lance rushed forward and pounded against the hand's armor. It pulled back and pounded forward a second, third, fourth time.

To Shinji felt like his hand was being smashed by a hammer. Not needing the distraction he shut off the pain receptors within his left arm. At the same time Unit 01's shoulder pylon opened and the Eva grasped the one weapon in its arsenal, a single progressive knife.

The progressive knife was a weapon with a blade oscillated at an intense speed, giving it cutting power strong enough to pierce the hide of an Angel. It wasn't much, but it certainly caught the Angel's attention as Unit 01 drove it into Sachiel's shoulder.

Sachiel roared in pain, breaking away from its attack and backing off slightly. Shinji took the opportunity to drive Unit 01's fist towards the vulnerable core, but the effort was for naught as his attack slammed into the unyielding force that was the Angel's AT Field.

'_Damn it! Getting though that barrier is going to be a real problem without enhancements._' That's when the Angel's eye's started to glow with a familiar power. "Oh Hell." Deadpanned Shinji just before the blast struck Unit 01, sending it flying backwards half a kilometer before it crashing into a building and effectively demolishing it.

Shinji groaned as he struggled to get the Eva back onto its feet, only to knocked down by a second blast, with a third, fourth, fifth, and sixth right on its heels. The force of the explosion dazed Shinji for a few seconds. Coming around he suddenly felt stabbing pains in his legs that threatened to put him under again if he didn't shut off sensation to them. A quick assessment told him that both legs had broken ankles where the armor was weakest as well as some long twisted piece of rubble piercing the back of the right knee. The left arm was a mess, the weakened armor having shattered completely, revealing the Eva's organic nature. And as if that wasn't bad enough the rest of Unit 01's armor was riddled with stress cracks from the multiple energy assault.

Bringing his attention back to the Angel, Shinji saw that it seemed satisfied with the damage it had inflicted upon Unit 01 and was back to blasting through the armor plating that protected the Geo Front.

'_No! If it gets to NERV its all over!_' He shouted mentally. "Damn it! Move!" He commanded the wounded giant, which shuddered upward for a moment only to slump forward "I need to protect the city! It's my purpose to fight the Enemy! I need to protect this world from the Enemy!!"

Unit 01 heard its pilot's cry and it responded, for it had the same purpose. The mighty titan's head snapped upward, its eyes blazing with power. The jaw restraints snapped apart like wet paper and the Eva released a mighty roar to the Heavens. Lowering its head Unit 01 saw its prey.

* * *

With a gasp Shinji's eyes snapped open. Confusion overtook him for a second as he took in his surroundings. As the confusion ebbed away and clarity set in, Shinji settled down. The room he was in was a standard hospital room, probably run by NERV.

His gaze shifted upward as he let his thoughts drift, the sound of cicadas in the background. Aloud he said, "Unfamiliar ceiling."

* * *

In another portion of NERV, within a room behind the cavernous expanse of the Commander's office that is off limits to all but Gendo Ikari a meeting was taking place. A meeting between Gendo Ikari and the five members of the Human Instrumentality Committee, the UN officials in charge of overseeing NERV and adjusted the budget based on the organization's performance.

In truth it was all a sham. The UN may be the ones who are officially in control of NERV, but that was only in name and on paper. When it came to dealing with NERV the UN was just a puppet, and the puppet master was the organization SEELE. The secret benefactors of the Katsuragi expedition, and who later would provide the stimulus needed for the creation of GEHIRN and manipulated who would be selected to be on the Human Instrumentality Committee. The members of SEELE were unknown and their goals a mystery to all but a handful outside their number.

It was in this meeting room where the Commander debriefs the UN about the confrontations between NERV and the Angels. As usual the discussions did not go well. It was only to be expected when such men were thrown together.

SEELE didn't trust Gendo, but at the same time they realized that they needed him. Gendo suffered the 'Old Men' because they had the resources he needed to accomplish his goals and at the same time had the resources to remove him if he ever lost value in their eyes.

It was an exhausting dance, and a lesser man would walk away from it looking years older. But Gendo Ikari merely looked annoyed as he returned to his office and sat down at his desk.

"How did it go Ikari?" Asked Sub-Commander Fuyutsuki who appeared from the shadows at Gendo's side.

The Commander sighed as he adjusted his glasses. "They threatened to cut our budget."

"Do you think they will?"

"Unlikely sensei. The Old Men know now that the Angels have appeared they cannot take any risks with the scenario. And taking away our money when we need it would do just that. No they will wait until repairs have been made to Unit-01 and the city, just to show us that we are still on their leash."

"Hmm." Mused the old teacher as he pulled out several documents. "We have the preliminary results on the Magi's analysis of the Third Child's synchronization ratio."

"Thank you sensei." Said Gendo, taking the papers, then setting them aside in favor of other matters.

Fuyutsuki raised an eyebrow in confusion. "Aren't you going to read it? You did ask for it."

"Later. I already knew that the Third Child would be able to synch with Unit 01 at a much faster rate than the First and Second Child can with their Evas. I just did not expect it to be so great. So while it is an anomaly, it is minor and warrants little attention. And I doubt the cause of the anomaly is anything that will negatively affect the scenario."

* * *

Shinji stood in a window lined hallway with NERV Medical. His gaze swept over the lush forest that surrounded the small lake that filled the Geo Front. Again Shinji couldn't help but wonder at the majesty and grandeur of the manmade cavern.

'_Or is it manmade?_' A frown graced his lips as Shinji considered the needed logistics To construct everything he has seen in the past twenty-four hours, and it simply didn't seem feasible.

Tokyo-3 was hardly a new city, having formerly been Hakone, but it had been considerably modernized and militarized since Second Impact. Then there was the construction of NERV's facilities and defenses. And finally he had to consider the Evangelions. They would have needed a considerable length of time and money to be built and tested.

Doing all that while at the same time digging out several cubic kilometers of earth, then undertaking a major landscaping endeavor to replicate the outside world? The costs of such projects would be staggering and probably be more time consuming then everything else, and the landscaping that created the lake and brought in the vegetation served no practical purpose aside from aesthetics. '_But what if NERV merely dug their way to what was already here…_'

Shinji's musing was cut short as he heard the sound of wheels. Turning he saw that it was Rei. "Excuse me nurse," he called to the woman pushing the hospital bed. "Would you mind letting Ayanami-san and I talk alone for a minute? I'll even take her back to her room for you."

The nurse had no problem with it and acquiesced to his request. When she had left Shinji took her place and pushed the bed along to its destination, while studying its occupant. Outwardly he noted that the First Child still wore bandages in all the same places as she did yesterday, and she seemed mildly confused at Shinji's request but ultimately uncaring. However inwardly Shinji was trying to establish contact with the nanites in Rei's system. A task that was proving to be rather troublesome. '_The nanites I injected were programmed to shut down once their objective was complete, but from the looks of Rei's condition their mission was far from over. So why can't I get in contact with them?_'

During his musing Shinji couldn't help noticing that Rei had yet to take her eyes off his face. "Do I have something on my face?" He asked.

"Why?" Asked Rei. "Why did you refuse to pilot Evangelion, and then accept to?" To Rei it was puzzling that anyone associated with NERV would refuse an order.

"Well technically I never refused to pilot the Eva. I was merely pointing out that the odds of a teenage male successfully piloting something as complex as the Eva for the first time when he didn't even know it existed several minutes before, against a creature that the JSSDF couldn't even slow down without the use of an N2 mine, were not good. I also asked what would happen if I refused to pilot. My father decided that he would demonstrate what would happen and called you in." Explained Shinji. "As for why I chose to pilot, well my reasons are my own." Shinji figured that Rei was the type of girl to be satisfied with such an answer, and she was.

However today something was nagging at Rei within her mind. "I remember something, before I lost consciousness. You said that you were keeping me safe."

'_She remembers that!_' "Like I said Rei, my reasons are my own. But yes I did pilot to keep you safe. It was clear that if I did not they would have made you pilot the Eva. And you were simply in no condition to do it. I can't even believe that they would even consider a plan that had a 100 percent chance of ending in your death."

"It does not matter. I am expendable." Rei said emotionlessly

"Don't say that!" Shouted Shinji so emotionally he jostled the bed, causing Rei to wince in pain. Shinji took some deep breaths and calmed down. "I'm sorry Rei. But you shouldn't say that. You shouldn't feel that way." His voice lowered and his eyes closed as memories from the past were called up. "That's how I felt years ago. I felt that I was useless, that I didn't have any worth. That if I suddenly dropped dead know one would care. And to be honest that could very well have been true. I had no purpose, nor was I anything special." Shinji's head picked up, his eyes opened, and his voice lifted with a bit of emotion. "But four years ago my perspective on life changed. When that happened I no longer thought of myself disposable. And I couldn't be happier because of it."

Rei was intrigued. The Third Child had thought the same as her in the past yet no longer did? Although she knew that Shinji did not know how if she died then there would be another to replace her thanks to the numerous spare clones kept in Terminal Dogma, nor that she was currently the second incarnation of the First Child. But still she couldn't help but wonder what it was that changed him. And she asked Shinji this as he pushed her bed through her room's door.

Chuckling Shinji responded, "Sorry Rei, but that would be my little secret. Maybe I'll share it with you someday. As for what I learned, well that is something you will have to experience yourself."

As Shinji said this he moved to stand on Rei's blinded right side to maneuver the bed into position, and has he did so Rei felt a slight prick so small that she wondered if it was just her imagination.

"Now Rei, I do believe you need your sleep." Rei registered these words as her eyelids grew heavy and sleep overtook her.

Shinji watched as the unusual girl fell asleep. Someone as injured as she was really needed to get plenty of rest, but it didn't hurt that his nanites were helping to induce sleep. '_Now then, let's get to work._' Keeping a hand on Rei to help insure there were no communication errors, he sent out his nanites to figure out the girl's secrets and what had happened to the first group.

Within 15 minutes he had found all of the deactivated nanites of the first group. It was odd because he found that they had begun repairs to Rei's body, and it was because of those repairs that Rei was even conscious today. Annoyed at the lack of progress he immediately ordered several of his nanites to bring back some of the deactivated machines.

Once several specimens were returned Shinji ordered a standard breakdown and memory dump. Across his eyes data images appeared. In his left eye were the images of the breakdown process and the examination of every single almost molecular sized component that made up each cell-sized machine. In his right eye was a detailed report on Rei's physical makeup that the original group had gathered before deactivation. For the most part it was pretty standard. She did have some odd pigment cells in her eyes and hair, thus giving her the unusual colors. Rei could also stand to have more protein in her diet. That's when a list of her organs and their conditions popped up and Shinji's eyes nearly bugged out of their sockets.

'_What is this!?_' He mentally shouted in surprise. '_It's impossible! This can't be right!_' Yet there it was. Most of Rei's organs were the same as any other persons, except for one. It was her womb, or rather her lack of a womb. In its place was another organ that shouldn't exist in a human, only in the Enemy or as NERV calls them Angels.

He didn't know what NERV called it, nor did he really have an equivalent word in Japanese or any other language he knew, but the race that built the nanites called it a _sisione_. And it was a very interesting feature of the Enemy, even more interesting than their core and barrier.

From the dissected bodies of the few Enemies that had been killed mostly intact came the discovery of the _sisione_ which was the source of the Enemies power. Or to be more precise it was a source of virtually unlimited energy. If it could ever be replicated it could be used as a devastating weapon. However the enemy seemed to know that and raided the site the first one captured was being studied. After that anytime a body of the Enemy was captured dead yet intact, it would decompose too quickly to be of any use to anyone.

'_Yet here is one perfectly intact, if seemingly not functional, within a human._' Shinji then frowned as he suddenly remembered Unit 01 which was an Angel without the _sisione_. '_So is she truly human?_' He wondered. To answer that question he pulled up Rei's genetic profile and gave it a quick scan. The results made him do a double take. '_If I am reading this right, and I do believe I am, then Rei, as impossible as it sounds, is half Angel._' This was getting to be too much. Incomplete Angels, human/Angel hybrids, giant 'manmade' caverns, and fortress cities. '_I need answers. But first…_'

Shinji immediately began recalling the nanites in Rei's body. Once they were returned to him he would begin reprogramming them. Because she was only half-Angel the nanites wouldn't try killing Rei, however she was just Angel enough that they wouldn't help her either, at least not now that they know what she is. But after a day or two connected to the main computer (his brain) they would then be ready to be returned to Rei to finish repairing her. And maybe once he got his answers, do more than just repairs.

* * *

"You'll be living alone?" Said Misato unbelievably.

It was later that day and Shinji had been discharged from the hospital. Currently he and Captain Katsuragi were going through the process to changing Shinji's residence from the house with his teacher to a place here in Tokyo-3.

A NERV official answered in the affirmative to Misato's question, stating that Shinji would be living in the sixth block of the residential district.

Shinji had no problem with it as it would allow him to work without interference, depending on whether or not he has to deal with any surveillance beforehand.

"Shinji are you sure about that?" Misato asked him.

Giving her a small smile Shinji answered, "Living alone is fine by me."

But it seemed it wasn't fine with Misato as minutes later she was on the phone with Dr. Akagi saying how Shinji would be living with her, as well as making several sexual jokes at his expense. Shinji though wasn't sure about it. He would be spending an incredible amount of time around his direct superior who presence could very well interfere his work. On the other hand his first and current impression of Misato didn't point towards a person who would be too troublesome to deal with. Perhaps he could even use her position to his advantage.

Hanging up the phone Misato turned towards her new ward with a big grin on her face. "Well Shinji it looks like you'll be bunking with me. And do you know what that means? A welcoming party!" She shouted excitedly.

Shinji smiled at the thought but he had to take care of some things first. "That's great Misato, but if you don't mind before we leave I'd like to visit with NERV's command bridge."

"Huh?" Was Misato's elegant reply. "Why would you want to see Central Dogma?"

"Well I just that that I should see the place that would be giving me orders in battle and to meet with the people I will most likely have the most involvement with." What he left unsaid was, '_And it will give me a great opportunity to leave some nanites to open the back door later._'

Misato didn't see any problem with the request, and began guiding him to Central Dogma. After half an hour and 12 wrong turns Shinji took the lead made two turns, took the elevator down three floors, walked fifty feet down a hallway, took another right turn, stopping in front of a pair of metal doors with the NERV logo underneath which were the words Central Dogma. And it only took 5 minutes.

Shinji looked back to Misato with a cheeky grin as he bowed and gestured for her to go first. Misato ran her ID card through the scanner and entered her password, all the while muttering about cheeky punks and labyrinthine buildings.

Upon entering Shinji couldn't help but whistle at the sheer immensity of the room. It looked large enough to hold an Eva.

"Impressive, isn't it Shinji?" Said Misato amusedly as she stepped forward towards several control stations where three individual in uniforms were working. One of whom had noticed the unexpected arrivals.

"What are you doing here Captain?" Asked the bespectacled one asked the Operations Director. "I thought your shift had already ended."

"It did Makoto." Answered Misato. "However my new ward here," she pointed to Shinji who had walked up beside her, "decided he wanted to see the place and meet your guys. Shinji this is Lieutenant Makoto Hyuga," she said pointing to the tech with glasses.

"Hey Shinji, welcome to NERV. And after last night I can gladly say it nice of you to join us.

"This is Lieutenant Maya Ibuki," this time indicating the mousy brunette and only woman of the group.

"It's nice to meet you Shinji."

"And the long haired rock-head is Shigeru Aoba," said Misato pointing to the long haired man with head phones on.

"Pleasure to meet you Shinji, and as a word of advice if you are going to live with the Captain you better know how to cook or else you won't be living much longer."

"What's That Supposed to Mean!?" Shouted Misato at the indirect insult.

Shigeru simply shrugged and said, "Let's just say your cooking is a little infamous to those who work with the technical division." In truth there were horror stories about Misato's collage days, most of which originated from a certain blond formerly brown haired roommate.

"My cooking is not that bad!"

"Maybe it isn't but better safe than sorry."

Shinji laughed at the sight of Misato on the verge of strangling her subordinate. '_Maybe I should divert their attention._' "It is nice to meet all of you. You three must have pretty important duties to work here."

"Yes we do Shinji." Said Makoto. "The three of us are in charge of running synch tests, monitoring the Eva and pilot during battle, assessing battle damage and making sure it gets repaired."

"Don't forget, Makoto, that we also in charge of monitoring the Magi, without which we wouldn't be able to do our job," added Maya.

This Shinji found intriguing. "Magi?" He asked the group.

It was Maya, the one with the best programming skills amongst the group that answered. "It's the Magi Super Computer System." She typed in a command on her council and called up an image of three turquoise squares connected by a ring with Magi in the center. "The Magi are three computers that utilized a sixth generation AI with the computers being named Melchior, Balthazar, and Casper respectively. The Magi run all of NERV's systems, and they're even hardwired into and control Tokyo-3's systems as well, so they in effect they 'govern' the city. They make decisions on what actions to take by voting between themselves."

"But weren't they built for the same purpose?" Asked a confused Shinji. "Then wouldn't they always make a unanimous decision?"

The question made Maya smile because it indicated that Shinji had a bit of knowledge about the subtleties of programming. "Normally that would be true Shinji, but each of the Magi was programmed with slightly different priorities, meaning that they each consider different aspects of any decision to be most important."

"I see," said Shinji. "_It's an efficient system. Being computers they won't care about any outside factors beyond the pertinent facts. They can't be bribed or threatened. However computers are notorious for ignoring the human factor, and very willing to write off the deaths of a hundred if it saves a thousand. And they can be hacked. Granted I have no doubts that these computers have the most powerful digital defenses ever created on Earth. And a sixth generation AI isn't easy to fool. Fortunately I know a couple of non-Earth related tricks._' "Would you mind showing me the actual computers that store the Magi?"

"You already have," answered Makoto. "Right now we're all on top of Balthazar."

Eyebrows raised in curiosity Shinji walked over to the computer councils which were indeed the edge of a balcony that over looked the three massive computers. "Amazing," muttered Shinji as he quietly let out a horde of nanites. By themselves they wouldn't be able to do much in the Magi, at least not without being detected. But they did give Shinji a backdoor into the system, and that was all he needed.

"Yikes," said Misato as she looked at her watch. "C'mon Shinji. We need to get going if we want to get the supplies we need."

"Alright Misato. And again it was nice to meet you three."

Shigeru smiled as he said, "No problem Shinji, and remember my warning." He barely dodged the pen Misato threw at his head, laughing all the way at his superior's expense.

* * *

Fifteen minutes later Shinji learned a very important lesson. Misato didn't need a giant alien monster hot on her heels and the fate of mankind on her shoulders to drive with reckless abandon at insane speeds. No she was perfectly capable of doing that on her own.

Before going to Misato's apartment they made a couple of stops. The first to a convenience store where Misato bought her weight in instant foods and beer.

The second stop was a real delight as it was an overlook on a cliff where Shinji was treated to the grand sight that is Tokyo-3 coming out of battle configuration. The buildings rising from the ground like new growth was awe-inspiring.

What was equally awe-inspiring was the sight of the interior of Misato's apartment, but for a completely different reason.

"This place is a mess!" Was Shinji's obvious understatement when she opened the door. The floor and table top were littered with the empty beer cans, liquor bottles, trash bags, microwavable food trays, discarded chopsticks, cardboard boxes, and other items that were clearly meant to be thrown away, not to mention the stacks of dirty dishes in the sink. Stepping further into the apartment Shinji caught a glimpse of Misato's bedroom and while it didn't have the same contents as the kitchen and entrance, the floor was essentially blanketed in clothes, magazines, and more beer cans.

"Sorry about that, I just moved in myself and I haven't had the time to clean for a while," said Misato apologetically.

'_Cleaned in awhile? Have you ever cleaned once since moving in here?_' "That's alright Misato. Tell you what, why don't you cook dinner while I tidy up a bit?" He offered.

Misato's grin told him that not only did she agree but that she felt that she had won the lottery. "OK Shinji, but would you mind putting the food in the fridge while I change?"

"No problem," was Shinji's response. As his new guardian went into her room he opened up the first compartment of the fridge, "OK, we have ice." Closing the first he opened the second, "Here we have snacks," he said seeing the junk food contents. Finally he opened the third. "And this one is stocked with fifty galleons of beer. Honestly how can she live off this?" He asked incredulously. Then he noted the second fridge on the other side of the kitchen/dining area. "Hey Misato! What's the other fridge for?"

"Oh, don't worry about that, he's probably still sleeping."

"Sleeping?" Shinji shrugged. Misato probably had a pet for which she had converted into a pet house for. She seemed quirky enough to do just that.

Once he was finished putting the food away he started cleaning off the kitchen table and countertop, at the same time Misato came out of her room and her apparel almost gave the teenager a nose bleed. He had to admit that the picture he had received did not do Misato justice and almost made him wish that she was fourteen years younger. '_Oh Well._' He sighed wistfully while moving into the living room. He didn't want to accidentally catch Misato's attention while he went about his work.

His cleaning of Misato's, and apparently now his, apartment wasn't entirely altruistic. The reason he volunteered to clean the place was because while Misato was busy cooking it gave Shinji time to root around for items made up of useful materials. Shinji had used up a lot of nanites in the past twenty four hours and he needed to replenish his supply. He had a feeling, scratch that, he knew that he would be needing every last nanite available in the days to come. Even if they weren't in his body.

That was why he was cleaning up the place. Whenever he found something made of the appropriate materials he would either absorb into his body or set it aside for later. When he absorbed something his remaining nanites would break it down on the molecular level until only the base elements were left. All useful materials would then be stored for processing.

Shinji didn't find much in the fifteen minutes since he started to when Misato called him for dinner.

During the meal Shinji learned several more things about his guardian. One, her culinary skills seemed limited to microwavable instant foods and curry. Two, she drank an unhealthy amount of beer. Three, unlike for most people where alcohol acted as a depressant, for Misato beer seemed to act as a stimulant.

After dinner the two played rock paper scissors to divide up the household chores. Misato was pretty good but when compared to a guy who had enhanced visual optic cameras for eyes that could slow the visual perception of time, and a nanite enhanced physical speed she just couldn't compete. Even when she tried cheating, like him. But Shinji was generous enough to split the chores evenly; he just chose to give the ones he didn't want to Misato.

"You should take a bath." Decided Misato once the chores were divided. "You didn't have one while in the hospital and baths not only clean the body but the mind and soul as well."

"If you insist Misato." In truth Shinji didn't need to take baths or showers, not when he had billions of tiny little robots that could pick any detritus material off his techno-organic body. But he found soaking in warm water soothing.

What he did not find soothing, more startling really, was the sight of a penguin right when he opened the bathroom door. Shinji blinked. The water fowl blinked. Shinji stepped aside and made a 'please continue' gesture. The flightless avian gave a brief 'Wark' of thanks and walked out of the room. Shinji's thoughts on the matter were, '_Misato is an odd woman._'

* * *

His bath finished walked into his new bedroom, which had a piece of paper taped to the door that said "Shinji's Lovely Suite." Inside the room was small, but adequate for his needs. One corner had his futon already set up for sleeping; another had a work desk for school work. Either then that the only items in the limited space were a number of boxes, most of which were marked fragile.

Opening up the largest boxed Shinji allowed his facial muscles to lift upward in a satisfied smile. Within the box were two desktop computers and a single laptop. These sleek machines did not look anything like what could be found in any electronics store around the world, and they weren't. They had started out their life like that but once Shinji got a hold of them he immediately took them apart and began the process of modifying the hardware, software, and outer casing to his specifications, before rebuilding them.

If anyone turned them on they would go through the standard boot up process for their standard counterparts, but that was just a masking program Shinji created so that any unauthorized users wouldn't learn anything about his capabilities or the capabilities of his machines. That program was also the only part of the computers that could be electronically scanned, because the masking program was the only part of the software that was still compatible with binary computer code.

One of the many gifts the nanites had blessed Shinji with was the knowledge of a computer code that was a hundred times more powerful, yet could be stored in the same amount of digital space. This made his computers technically more powerful and efficient than any contemporary supercomputer, but the sheer processing power controlled by the Magi would make them a tough nut to crack.

That's where the nanites he left in the Magi came into play. They were programmed with a tracer program that would leave a trail in cyber space for Shinji to follow back, and should leave a crack in the security software that he could slip through.

Taking the computers out of the box he set them up on the desk top with a homemade monitor set up in between. The laptop Shinji set off to the side, he wouldn't be needing that yet.

With the computers set up Shinji opened up another box and pulled out a smaller box. Within the box were a number of small disks about three centimeters wide and a half-centimeter thick. He pressed one disk against each all where it adhered itself. He activated them and some basic information flowed before his eyes for a few minutes. When it stopped he was a little surprised, there were currently no electronic surveillance equipment within their working range. '_Even if there isn't any surveillance currently but I leave them up. Don't want anyone just sneaking in here and messing with my equipment without my knowing._'

The disks were an item of Shinji's own design, and were very handy tools, especially if someone wanted to keep their plans secret. Their first function was to sweep for anything like listening bugs and video cameras. Their second function was to monitor the area so that no one could enter the room and do anything without Shinji finding out.

The next item to be unpacked was a large plasma monitor about sixty centimeters long and forty-five centimeters wide. Using the same adhering technology as the disks Shinji placed the monitor directly opposite of his computers. This device was relatively simple, when turned on it would show a picture slide show, or if set right a psychedelic blending of colors normally only seen on a hippie's t-shirt. But like Shinji's computers this was just a mask. Its true function is to pick up any wireless signal, like satellite TV, a cell phone call, that sort of thing. It could also could receive a special signal from the computers which it could then display as a holographic projection which could be physically manipulated thanks to sensors in the screen (think of something similar to what Stark used in the Iron Man movie).

After setting up a few more devices Shinji was ready. Sitting down Shinji shut off the masking program, changing the screen from the background of an ordinary commercial operating system to a purple backdrop across which lines of sigils scrolled across. Closing his eyes Shinji pressed his palm flat against the screen and uttered two words. "Log in." Shinji could feel his consciousness transfer from his body to the realm of cyberspace.

Moments later he opened his eyes to a sea of data composed of purple sigils. His body had changed, still maintaining the shape of a human, but everything below his shoulders appeared to be made of lines of blue sigils. Satisfied that the transition from his body to cyberspace was a success he looked forward and gave his command. "Initiate gateway connection. Begin trace."

With those words an opening appeared in the data around him, through which he could see a tunnel through which green lines of binary code soared. Before his feet appeared a red path appeared. Smiling he stepped onto the path and his digital body suddenly rocketed forward out the opening and into the network of Tokyo-3.

His tracer program was fast and efficient leading him to a wall of red data that could give the legendary walls of Troy a run for its money in the size department. This was the security that protected the Magi from outside hacking. Shinji stopped to examine it, reading the ones and zeros like most people read newspapers.

'_This is an impressive system. If I tried getting in the traditional way it would take months if I was trying to avoid detection. Brute force is out of the question, and it would take a considerable amount of time to crack the algorithms. Good thing I made myself a back door._' Reaching out Shinji touched a seemingly random byte of code, only for the green zero to turn blue and shift into one of Shinji's sigils. Touching several more bytes Shinji activated the code his nanites had spliced into the security system, opening a door in the wall.

Shinji smiled as he floated through the door. Once through the world suddenly changed from a sea of data to a replica of the Geo Front. Even his body had changed and he found himself in his plug suit. "Well wasn't quite expecting this. Most digital realms aren't nearly this complex. Kudos to the programmer."

By happenstance Shinji had appeared right next to the entrance of NERV. Walking down the corridor, passing programs in the form of faceless employees of NERV, Shinji wondered where in this labyrinthine building he would find what he wanted to know. '_Well if the inner workings of the Magi mirror the real world, then the most logical place would be Central Dogma. So I might as well start there._' With that in mind Shinji made his way to the control center of NERV, and possibly the Magi.

As luck would have it that the core of the Magi actually was in the equivalent of Central Dogma. And where Shinji found the first deviation from normal. A very big deviation. For in place of the control stations of the three techs he met earlier, there were three blocky, metal, throne-like chairs upon which sat three women. Moving closer to them he saw that each had the same face, brown hair, and a strong resemblance to a certain head of Project E. Although their style of hair and dress were quiet different.

The one on the right wore a skirt, button up blouse, and white lab coat with her hair cut short, much like the blond Dr. Akagi. The female in the middle wore a longer skirt, yellow blouse, and an apron and her hair was longer but tied up in back. Finally the woman on the left, and woman was an accurate description. She was dressed to kill in a little black dress with matching pumps, and her hair was as long as the woman in the middle but left down.

The three appeared to be sleeping with their eyes moving as if they were in REM sleep. As he took a closer inspection Shinji was startled when he saw that the woman weren't just sitting in the chairs but were hooked up to them.

Frowning Shinji extended his hand and a blue light shot forth shining on the woman. It only took a few minutes for Shinji to understand. '_Incredible! Those women are the core of the Magi. They are the programs which make all decisions and control everything. But these are far more advanced than a level 6 AI. They could be fully sentient. But_ _those chairs. They're limiters. Clearly installed before activation or those gals could have shrugged off their influence. Now the question is do I want them to be fully aware? If they're grateful it could be a great benefit. Well here goes nothing._'

Extending his hand forward again another beam of light shined on the limiters, but instead of blue this one was red. However as he began rewriting code alarms started wailing and lights flashing emergency red came on.

"**Warning Unauthorized Action Detected! Initiated Security Procedures!**"

"Oh Hell!" Cursed Shinji. "Sorry ladies but it looks like we will have to try again another time!" He shouted as he sped towards the exit like a bat out of hell.

* * *

Within the real Central Dogma two techs looked over the screen as a message they had never seen before appeared. Limiter

"Do you know anything about program L-913920518 and why someone would want to hack it?" Asked one tech to the other.

"Nope, never heard of it. But whatever it is I think this alert is just a bug in the system. According to this the hacker was here in Central Dogma doing it and there's no one here but us."

"Hmm, guess we'll have to talk to Dr. Akagi in the morning."

Unfortunately for these two techs Section 2 was on their way to apprehend everyone in Central Dogma, by order of Commander Ikari.

* * *

Within 'Shinji's Lovely Suite' Shinji's eyes calmly opened as his mind returned to his body. '_NERV has a considerable number of secrets. Eva. Rei. The Geo Front. The Magi. And the Angels. It's going to take time to discover the truth behind them all. But right now it is late and sleep is an enjoyable activity when my body has to focus on nanite production._' With that Shinji got up from his desk, changed into some sleeping clothes, and plopped down on his futon, his mind entering sleep mode in seconds.

And then he dreamed. He dreamed of a race so similar to humans stuck in a seemingly endless war. Of giants clashing with titans in a battle of supremacy. Of purple haired race car drivers. And he dreamed of an innocent blue haired angel.

* * *

**Author's Notes:** OK I am going to be honest here and warn you all that I know little about how to program computers and accompanying terms so I am just making stuff up here.

Hope you all enjoyed the chapter.

**Please Read and Review.**


	3. Future allies

**Cyber Shinji**

**Disclaimer:** I do not own Evangelion.

"Talking"

'_Thoughts_'

"_Radio_"

**Location

* * *

  
**

**Chapter 3**

"_OK Shinji, just position the target in the center then squeeze the trigger switch on._" Instructed Dr. Akagi as Shinji watched a targeting triangle and triple lines center on the scope's screen before turning into a targeting circle with the designated Third Angel in the center.

Of course if that had been a real Angel in a real Ritsuko Akagi wouldn't be the one speaking to Shinji, nor would she be so calm. No this was all just a simulation created based on Shinji's battle with the real Third Angel. The latest in a long series of simulations the administrators of NERV had had Shinji participate in. During these simulations Shinji had learned a considerable deal about practical use of the Eva. Such as the location all of the armament buildings, emergency power junctions, recovery zone, and other areas of Tokyo-3 that had been designed to aid the Eva in battle.

He also learned how the Eva receives electricity through an umbilical cord connected in the back. Without it the Eva would resort to an emergency battery, which only work for one minute at full power and five minutes in minimal gain mode. It wasn't a lot but it was the best NERV could do with their current battery technology, and was one of the projects he was working on in his spare time.

But without a doubt the most useful thing Shinji had learned was how to generate an AT Field to both defend himself and to neutralize an Angel's AT Field.

Today however the training was just a simulation of Shinji in Unit-01 aiming the large pallet rifle at the simulated Third Angel. For the two dozenth time this week alone. It was sufficient to say that Shinji was bored and more than a little annoyed. Shinji understood the importance of this type of training, the delay caused by the synch ratio meant that he couldn't rely on instincts or previous weapons experience. No what was annoying him was the fact that in every single simulation the Angel never moved.

Sure it would appear in different locations, sometimes uphill, sometimes downhill, sometimes on the west side, sometimes on the south side. But it never moved. It did not attack. It did not try to defend itself. It was a statue.

'_But not this time._' With an amused grin he wirelessly connected with the computer on the simulator observation deck, one of the many outlying systems that were slowly falling under his sway. '_Initiate program DDR Break._' "Center the target and pull the switch." He said as the targeting computer centered in on the Angel and he released a burst of simulated bullets at the Angel. But this time instead of just standing there the Angel ducked to the left. A second burst and it docked to the right. A third burst and the Angel dodged, by moon walking.

'_Stop the simulation!_' Shouted Ritsuko, having recognized that the Angel had started break dancing.

Shinji sighed as he watched as the Angel and the city of Tokyo-3 disappeared just as the Angel was starting to do that move where you spin on your back. '_Too bad, I wanted to see it try the Robot. Oh well, I think I'll choose a nice waltz next time. Maybe I'll even join in the dance._'

* * *

**Simulator Observation Deck**

"Wow Rits, I didn't know you could program the simulation to do that." Complemented an impressed Misato. "When you decide to do that?"

"I didn't," responded the bottle blond hotly as she began typing furiously at a console. "I've been far too busy with the addition of monitoring Shinji's training added to my regular work load to even think up something like this, much less program it."

Misato blinked at her friend's irate declaration. "Then was it you Maya?" She asked turning her attention to Ritsuko's prodigy and the second-best programmer in NERV, that she knew of.

"Sorry Captain, but I'm not nearly good enough to program such fluid movement. Besides most of my free time has been eaten up by helping Akagi-sempai." Explained the mousy brunette.

"Then who did this?" Asked a confused Operations Director.

"It's a hacker," answered Ritsuko. "A lot of our systems have been twitchy lately. At first it was mostly little things like problems in the door's sensors, clocks displaying the wrong time, lights suddenly switching off. But recently more substantial problems have been cropping up. Found it!" She suddenly declared.

"What is it Sempai/Rits?" Asked the two other women at the same time.

"I found the problem. Looks like someone hacked in and rewrote a portion of the simulation's Angle movement algorithm. Sigh, this is undeniable evidence that someone has found a way around our security. They don't seem to have any malicious intent, but if they changed this then who knows what other damage they may have unintentionally done."

"So what're we going to do about it Rits?"

"There's no other option. We're going to have to isolate all our systems and run a thorough diagnostic on all computers within NERV. Top Priority going to the Magi.

Within the Eva that stood in the stark white simulation room, Shinji grinned as he heard those words. '_One step closer._' He thought.

* * *

**Tokyo-3 1****st**** municipal Junior High**

The next day Shinji, after saying his goodbyes to Misato and dropping off the burnable trash, made his way to the Junior High school that Misato had enrolled him in. By what he assumed was coincidence, and something he had been too busy to check, he had ended up in Class 2-A, the exact same class as Rei. And so, as what was becoming customary over the past few days since he started attending the first thing Shinji did when he walked through the classroom door was head straight for Rei's desk, where she always was no matter how early Shinji was, interrupt her window gazing with a hearty good morning. And his efforts were being rewarded. She now gave him a full five seconds of her attention while giving her own 'good morning' before turning back to the window.

It used to be only three seconds with no 'good morning.'

Shinji was a little disappointed with himself. It had been two weeks since he had first met the girl and fellow Eva pilot, but she was still wearing bandages around her head covering her right eye, and her arm was still in a sling. His disappointment stemmed from the fact that he had yet to finish reprogramming the nanites to a point where they would heal her injuries. But the little buggers were proving difficult in that regard. Because of her half-Angel nature the nanites core program made them hesitant to offer her any aide. But if his estimations were right then it wouldn't be too much longer before they will work for her. Until then he would just help her mind instead of his body.

At least now that he was going to school and spending more time outside of NERV he had more time to work on his numerous projects, especially with the teacher of this class.

The old man who taught the class seemed absurdly focused Second Impact and its effects on the world. All day he would just drone on and on with only calling on a student once in a blue moon. What was weird was how he managed to incorporate that constant history lesson into the math, science, and languages classes.

But it worked to Shinji's advantage.

Several seats behind Shinji, a boy by the name of Kensuke Aida was keeping himself busy before class started by playing with a model of a VTOL fighter jet, including making the sounds, while recording it on his camera. His fun however was interrupted by a girl who wore her brown hair in pig-tails.

Putting down his toys the boy asked, "What's up Class Rep?"

"Did you deliver the printout I gave you yesterday?" Asked the Class Representative, Hikari Horaki.

Kensuke grew noticeably worried as he stuck his hand in his desk while trying to deflect the question. "What? Uh, well there wasn't anyone home at Toji's place."

"Aida-san," Hikari said in a tone that was a mixture of a disappointed mother and irritated military officer, "aren't you Suzuhara-san's friend? Aren't you just a little bit worried about him?" With each word sunk further into his seat, not unlike a child being scolded after having been caught with his hand in the cookie jar.

"You don't suppose he was injured do you?" Kensuke asked when Hikari had finished.

"What? You mean in that giant robot incident?" Shinji's attention perked up from the lines of mathematical equations on his computer, interest in the two students' conversation almost visible on his face. "The TV reports all said that nobody was injured."

"No way." Countered Kensuke. "You saw that explosion. And with all the fighters scrambled to fight, I bet at least ten or twenty people were injured. There may have even been a few fatalities."

At that moment the classroom door opened, admitting a boy Shinji had yet to meet, meaning that he was probably Toji Suzuhara. Shinji looked at the track suit clad boy and immediately thought '_Jock._'

"Hey Toji," greeted Kensuke.

"Hey Kensuke," returned Toji. Looking around the rather empty classroom he asked, "Where is everyone?"

"They've either evacuated or transferred to other schools. After that battle inside the city no one seems interested in sticking around."

"Yeah, you're probably the only one who's actually enjoying the chance to see a real war."

"That's true," admitted the military otaku. "Speaking of which, where have you been? Did you get involved in the war?"

Toji's response was distant, drained of emotion. "No, but my little sister did. She was crushed under a pile of debris. She survived but she's been in the hospital ever since. Because my dad and granddad can't leave the lab so if I'm not with her she's all alone." His voice hitched up, anger suddenly dripping from every syllable. "That robot's pilot was really dumb! How could he wreck our own city! It makes me so angry! What did he think he was doing!?"

"Speaking of the pilot, did you hear the rumor about the transfer student?" Whispered Kensuke into his buddy's ear.

'_A rumor about me?_' Thought Shinji. '_Why haven't I heard anything?_'

"What transfer student?" Asked Toji.

"Him over there." Kensuke indicated with a nod of his head towards Shinji who was typing away diligently on his computer. "He transferred while you were absent. Right after the giant robot incident. Don't you think it's a bit of an odd coincidence?"

More might have been said except that was when the teacher made his appearance.

"All rise, bow, sit," commanded Hikari in a fashion similar to a drill sergeant.

With class started the teacher began his lecture on the events of Second Impact and its effect on the world. Shinji wasn't really paying attention, it simply wasn't necessary to listen to such a lecture when you had your history textbook, all your textbooks for that matter, memorized after looking through them once. Instead Shinji was using the school computer to exchange e-mails with a Dr. Yamato, whom Shinji had found a reference to in one of the less restricted computers connected to the Magi.

But in the middle of his typing a message appeared on his screen saying that he was receiving an I'm over the school network. The sender of the message was anonymous.

Anonymous: Are you the pilot? Y/N

Raising an eyebrow in curiosity Shinji took a look around the room to see who was sending the message. His attention was drawn to two cute girls in the back who giggled and waved to him. However it was not lost on Shinji how a rather grumpy Toji was sitting behind them. One of the two girls typed into her computer and a new message appeared on Shinji's screen.

Anonymous: Well, are you?

Shinji spent a second mulling over what he should say in his head. '_Should I say yes or no? NERV never specifically said that the fact that I am a pilot is confidential. On the other hand if word gets out that I pilot a giant 'robot' in a school full of teenagers then I will probably be swarmed by people wanting to ask question about the Eva and NERV. But will I really lose anything? No. Will I gain anything? Nothing that I can see yet, but who knows. But first…_'

CyberShinji: Why would you think that?

Anonymous: Since the incident several people have transferred out, but you transferred in right after. Kind of logical isn't it?

CyberShinji: Not really. It is merely guessing based on unsubstantial evidence, especially when several known facts about me would logically contradict it. A more logical assumption would be that I have merely have a connection to someone that moved into Tokyo-3 who **might** have something to do with the robot.

Anonymous: So you're not the pilot?

CyberShinji: I never said that. To satisfy your curiosity girls, and undoubtedly the curiosity of the rather grumpy looking guy behind you that I suspect put you up to it, yes I am the designated pilot of Eva Unit 01.

The moment after the message was sent, every student rounded on Shinji, with the exceptions of Rei, Hikari, Kensuke, and Toji, talking excitedly and loudly. This was a lesson to Shinji to make sure that the I'm board isn't an open chat room before responding to anything else.

Oddly enough the teacher completely ignored the uproar and continued on with his lecture. He was looking out the window at the time so Shinji suspected that he wore hearing aids that were turned off.

"Quiet down everyone! Return to your seats!" Commanded the Class Rep, who was completely ignored beyond a few comments about how bossy she was.

"How did you get chosen?" Asked one girl.

"Did you take a test?" Asked another girl.

"Weren't you scared?" Asked a third girl.

"What's the cockpit look like?" After the fourth girl asked a question, Shinji suddenly noticed that there were a lot more girls than guys in this classroom. And almost all of them were now crowded around his desk. (It's weird by while doing research I found that the guy to girl ratio in class 2-A is 1 to 3)

"You said you were the pilot of 'Eva Unit 01' is that what the robot is called?" Asked one of the few guys.

Finding a pause in their questioning Shinji answered in order. "I was selected by something called the Marduke Institute. I did not take a test they merely said that I was chosen to be a pilot. I was scared. The cockpit is an Entry Plug and it is a little hard to describe. And yes Eva Unit 01 is what I pilot." OK so technically some of that stuff was classified, but it was no skin of his nose if others knew such basic information. But the fact that he answered seemed to increase the class's interest.

"Hey what's the robot's main weapon?"

"A progressive knife, a bladed weapon that oscillates at ultra-high frequencies to increase its cutting power."

"What does the 'Eva' use for power?"

"Electricity from the city's power grid, but research is being done to make it more independent."

"Can your robot transform into anything?"

"No."

It was not lost on Shinji that after he answered every question Kensuke Aida would type furiously into his computer. '_What are you up to?_'

The bell rang, which the teacher actually heard dashing Shinji's hearing aid theory, and class was dismissed.

* * *

**Tokyo-3 1****st**** Municipal Junior High School**

Being as resourceful as he was Shinji was able to get out of the classroom and avoid the mob of students eager to get on the good side of the Third Child so that he would regale them with stories about the Eva. His chosen hiding spot was the school grounds behind the gym.

It wasn't good enough.

"Hey new guy!" Called Toji's voice from behind.

Shinji turned and saw a fist heading straight for his face. With reflexes just this side of inhuman Shinji snatched the fist with his left hand. "Hostile, aren't we?" He asked rhetorically to the two boys that had joined him behind the large building.

"Shut up! I gotta pound ya to work off my anger!" Shouted the jock of the two as he valiantly struggled to release his hand, but the new guy's grip was like a vice.

"You don't want to do that." Said Shinji. "You'll just end up feeling worse."

"I'll be the judge of what makes me feel better!" Shouted Toji, having given up on freeing himself he swung his left fist. This time he struck home, signaled by a resounding 'CRACK.' "GYAAAHH!"

"I warned you." Said Shinji as he released the boy's other hand.

"What the hell are you made of!? Steel!?" Asked Toji as he nursed his throbbing hand, which Shinji didn't think was broken.

Shinji chuckled. "No, I'm not made of steel." '_Not even close to actual steel._' "Tell me did you actually think hitting me would make you feel better?"

"After what happened to my sister because of you? Yes!"

"Sigh, then let me ask you this, what was your sister doing outside of the shelter in the city? I know for a fact that all civilians were given a warning several hours in advance and that by the time the Angel arrived everyone had evacuated to the shelters. So why wasn't your sister?"

"Shut up!"

"Perhaps you do know why, and that knowledge has created a guilt that eats away at you. You seek absolution from this guilt by finding another to take responsibility. Thus you have turned your attention to the pilot of the Eva that was the direct cause of your sister's injuries. Injuries she would not have if she had been where she was supposed to be."

"Shut up!"

"But to say that none of the blame rests with me would be folly. I chose to pilot the Eva to destroy the Angel and protect humanity. Despite the fact that there were circumstances beyond my control the prevented me from making full use of Unit 01 thus more efficiently dealing with the Angel, thus causing injury to your sister. If I had been paying more attention to my surroundings I might have noticed her and avoided causing her harm. For this I am sorry." Shinji said with a bow.

"Shu…What?" Said a now confused Toji at the complete reversal of blame.

"I chose to pilot the Eva; thus is my duty to protect the people of not only this city but of the entire world against the threat of the Angels. Even though that was the first time I piloted the Eva that is still no excuse to allow anyone to come to harm."

"Wait," interrupted Kensuke, "that was the first time you ever piloted? What about training?"

"My training didn't start until three weeks ago, **after** my first sortie. And it was only the day before that I was ordered to come to Tokyo-2 where an agent of NERV picked me up, brought me here under fire of the Angel. Less than a full hour before my the battle began I was informed that I had been selected to be the Third Child and Eva pilot." Explained Shinji.

"What kind of idiots sends out an untrained guy in a giant robot?" Asked Kensuke. "I'm surprised you didn't destroy the entire city. Don't they have any others?"

"Two actually, but one was heavily injured and could not pilot and the other lives on the other side of the world. I was the only viable option."

Toji had been listening and his temper had been given enough time to overcome his earlier confusion. "That doesn't make the fact that my sister got hurt alright! And you saying sorry ain't enough either."

"I know which is why I'm going to make sure your sister receives a treatment that will have her out of the hospital in a few week, maybe even days."

That was enough to stop an further rants from Toji. "Really?" He asked hopefully.

"Yes, I am in a position to provide your sister medical treatment that is more advanced then what she is currently receiving in the Tokyo-3 hospital. However this method is top secret, and cannot be disclosed to anyone at the hospital without permission. Do you accept?"

Toji thought about it for a few moments. He could tell Shinji was holding something back. "What kind of treatment is this?"

"I'm sorry but I won't be able to disclose that with you until it is time for the treatment. However I can promise you there will not be any invasive surgeries, untested chemicals, or dangerous radiation. Just a simple proven treatment that due to availability issues keeps it from being used by the general public."

Toji frowned, but the temptation of having his sister healed and out of the hospital was too much. "Fine, but I'm going to watch the whole thing, I want to know exactly what it is that will happen before anything is administered."

"That is perfectly acceptable."

With that Toji walked with Kensuke trailing behind. Though just before he left Toji looked back and with a growl said, "I still don't like you."

Shinji watched the two walk away. "Is there anything I can do to help you Rei." He asked the girl that had walked up behind him.

"There is an emergency. I'll report in first." With that she turned around and ran off.

A second later the Angel alert siren went off.

"The Enemy approaches. Will it posses form similar to the last? Or has it changed to better combat the Eva? I'll know soon enough."

* * *

**Tokyo-3**

The Angel's form had indeed changed from that of its predecessor. Where the Third had been green, spindly, and humanoid in shape the Fourth was purple, bulbous, and insectile in appearance. Also unlike the Third, the Fourth had some limited flight capabilities and moved much faster than its predecessor.

At the moment the JSSDF was attempting to stop the Angel with their standard anti-air interception weapons. As Deputy Commander Fuyutsuki said, 'It was a waste of tax payers' money.'

But that didn't concern Shinji. He knew that just like before when the military exhausted their supplies and had nothing left to throw at the Angel, then they would call for NERV to mobilize an Evangelion.

"_Remember Shinji, stick to the plan. Neutralize the Angel's AT Field and take out the Angel, just like in the simulation._" Said Misato

'_Somehow I doubt it will be that simple._' Thought Shinji as he waited in the Eva that had been moved to a catapult. '_This Angel looks nothing like the last one and its abilities are probably just as different._'

Soon enough NERV was ordered to mobilize and Misato gave the command for the Eva to launch. On the surface Shinji deployed his AT Field, neutralizing the area that the Fourth's would work in.

"Well here goes nothing." Breathed Shinji as he rounded the corner of the Catapult chute, targeted the Angel and fired a barrage from the pallet rifle he was equipped with. However even without an AT Field the Fourth's hide was too tough for the rounds which only managed to kick up a cloud of smoke.

"_Idiot, you just hid the Angel in your own smoke!_" Berated Misato.

'_Not to my eyes. Thermal imaging active._' The color scheme of the world shifted as Shinji changed his visual perception to see heat radiation, revealing the Angel hiding in the smokescreen. Seeing the attack it had prepared Shinji commanded Unit 01 to leap backwards, narrowly avoiding the white-hot energy whips. But that didn't save the catapult or the empty rifle Shinji had discarded.

"_Shinji, we're sending you another rifle. Take it!_" Ordered Misato.

Shinji shifted his eyes back to normal and watched as the Angel emerged from the smokescreen, whips flailing about. "Sorry Misato but a rifle won't do much good against this thing." As he said this Shinji used visual sensors to get a reading on the whips. '_Can the Eva's armor hold out against it? It can, but not for very long. But if I use my time wisely then I can get close and smash the core. But there's not enough room here in the city proper. I need to go somewhere with more space so those whips will cause as little damage as possible._' Looking around he spotted a clear area only a few kilometers away. '_And that looks like a perfect spot._' With that thought Unit 01 turned tail and ran for all it was worth.

"_Shinji! What are you doing!?_"

"Just getting a little extra leg room." Responded Shinji as he made the Eva leap to avoid another whip. Unfortunately it didn't miss entirely and slashed through the umbilical cord. In both the Entry Plug and Central Dogma a large timer appeared, starting at five minutes and counting down. "Well that's problematic. Guess I'll just have to conserve my movement." With that he forced Unit 01 to make a massive leap with everything it had put behind it. With a flip and a spin in the air the Eva landed on its target mountain facing its foe, only for Unit 01's foot to slip on a loose patch of ground causing the Eva to fall on its back.

"Oww! Did not mean to do that. Now where's that…Huh?" Movement in the corner of his eye caught Shinji's attention. What he saw was Toji and Kensuke cowering in the gap between the Eva's fingers. "What are those two doing here?" He asked, though he had no time to contemplate as the Fourth Angel used its speed to appear before Unit 01. "Oh Great," muttered Shinji as Unit 01 grabbed hold of the whips to prevent them from flailing.

Outside the Eva.

"Why isn't he fighting back?" Asked Toji.

"He can't because we're here. If he moves we'll get crushed." Wailed Kensuke.

Back inside.

'_This is not good._' Shinji thought. '_If I move then those two…_'

"_Shinji, open the Entry Plug. Let them in. Once you've got them make a temporary retreat. We'll try again later._"

'_I'll obey part of those orders Misato, but if you let the Enemy have too much free time you'll only regret it later. If we're still alive._' With those thoughts in his head he shut down the immediate controls, which shut off the lights, and brought the Entry Plug partially out of the Eva.

Outside Toji and Kensuke's heard Misato's voice ordering them to get in. The two obeyed. "Ug its wet, is this water?" "AAGH My Camera." Although they did it under a bit of protest.

With the two inside command control was restored and as the lights came on the two saw Shinji struggling to hold the Angel at bay. "I can't believe you two, especially you Toji. I would have thought that after what happened to your sister you would have been smart enough to stay in the shelter!" Berated the pilot. '_Not good, my connection with the Eva is fuzzy. Those two must be causing interference. But at least now that they're in here…_' With a mighty heave on the arm whips Unit 01 threw the Angel off of it, using the Angel's ability to fly to its own advantage.

"_Alright Shinji. Now retreat using emergency route 32._"

'_Sorry Misato, but there's no time_.' With a mental command all the radio system within the Entry Plug shut off. "You two never heard that last order." He said to Toji and Kensuke. "That Angel needs to be taken down now before it can cause anymore damage, and you guys get a front row seat."

"So Cool," exclaimed Kensuke. Then Toji noticed the timer. "Uh Shinji, what's with the countdown?"

"Oh that's just how much power the Eva has left." Responded Shinji casually.

"WHAT!? You're going to fight that thing with less than three minutes of power!?"

"You're right. I should change that." Suddenly the timer reset itself to five minutes and restarted the countdown. "It's not much but right now it's the best I can do. Again you two didn't see that."

"Why not?" Asked Kensuke.

"Because the battery should almost be dead not still have another five minutes. Now to take care of that Angel." With a leap Unit 01 slid down the mountain towards the Angel.

As the Eva got close Shamshel lashed out with its whips, which Shinji avoided by tucking down and rolling. Using the momentum of the roll Unit 01 sprang to its knees, progressive knife in hand, thrusting its weapon into the core of the Angel. Sparks flew as the oscillating blade pierced the crystalline orb that is the heart of an Angel.

Shamshel retaliated against the attack, its whips slashing at the Eva's armor, melting and even cutting it off to get at the vulnerable hide beneath. Shinji urged with all his will for Unit 01 to push harder, and his efforts were rewarded as a spider web of cracks splintered from the initial cut. The core lost its color and the whips faded away.

Pushing the Angel away Unit 01 freed its knife. "Whew," breathed Shinji. "I was a little worried there." With the Angel dead Unit 01 calmly walked to the nearest catapult.

* * *

**Misato's Apartment**

Shinji walked into his room contently. It had been a long day after the fight with the Angel. The debriefing alone took hours, what with Shinji disobeying a direct order. Fortunately the Magi had recorded the 'radio malfunction' as happening just before Misato issued her last orders, so since Shinji never heard them, he wasn't liable for disobeying them. Then there was the fact that Unit 01's battery lasted longer than it was supposed to. This time it was attributed as a favorable glitch in the battery, a glitch that should be studied to help the project to extend the battery life.

No one bothered to debrief Toji and Kensuke. They were just chewed out and given a very stern warning that if they ever tried that again they would be thrown in jail. Yet that was light compared to what Hikari did when she got hold of them.

Overall the only person who wasn't satisfied was Ritsuko Akagi. As if she had some sort of sixth sense concerning those three computers, she had ordered the Magi core isolation and scan for tonight, just to make sure that the results the Magi gave at the end of the battle were really the Magi or some sort of hacker messing with them. And this was precisely what Shinji wanted

Shaking his head to focus himself Shinji sat down at his computer. "Log in," he intoned.

* * *

**Magi**

Disguised as a sweeper program, which looked like NERV maintenance crew, Shinji followed along at the back of a line of sweeper programs. External security, while improved since he first started sneaking into the Magi, was no more difficult than usual, his backdoor having avoided detection. But internal security had dramatically tightened. Numerous temporary programs that looked like Section 2 down here were set up everywhere making sure that none of the programs were doing anything that they weren't supposed to. They were brought in after Shinji's first night, on order of the Commander. And they had been a real hassle to Shinji. Sure he could get away with little things in more outlying systems, but if he wanted access to do more then he would be need them gone or on his side.

But today they were witnesses that he will use to his own advantage. After all, they were only watching out for programs that were doing things that they weren't supposed to be doing, not a program doing exactly as it should. And as far as they knew he was just another diagnostic program going about his duties.

At each door and hall junction another program would veer out of the line and head on a course towards one of the different components of the Magi. Shinji just kept going towards his goal. The core of the Magi.

Once there he saw that the three women, which he now knew were exact replicas of Dr. Naoko Akagi, Ritsuko Akagi's mother, were all guarded by two security programs. Not that it mattered.

Grinning Shinji placed his hand on one of the limiters and said, "Initiating Scan." This was not the same scan as when he first came here. That scan was just to read the program, discover their function. This time he was scanning each limiter program to learn their code; the algorithms that make them work. '_Once I know where every zero and one is for each limiter's I can then begin the third and final phase._'

* * *

**Misato's Apartment**

Once he had finished the scans Shinji returned to his body. Looking at the clock he found it read 2 a.m. '_How that didn't take as long as I thought. I only started at 10. Well I guess I'll do one more thing before going to sleep._'

Shinji called up a letter writing and encryption program and began typing a letter to his latest correspondent.

_Dr. Yamato_

_I am glad to pleased to say that I have finished my part for the project. As such the program is now ready for installation. I know I am only a junior member, having only joined a 11 days ago, however I insist that I be brought up to do the installation itself. The subject of my code is a very delicate matter that I will not trust to anyone else; however once it is complete then my involvement will no longer be necessary and everything can be left in the capable hands of you and your team. And once you have completed it I am sure that there will be no one able to refute the value of the Jet Alone.

* * *

  
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**Author's Notes:** A little shorter chapter this time, but I just felt inspired today to write this chapter and I wanted it out quickly.

**Please Read and Review.**


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